5C9S | pdb_00005c9s

Crystal Structure of the C-terminal domain of Rrp5

• PDB DOI: https://doi.org/10.2210/pdb5C9S/pdb

• Classification: GENE REGULATION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-28 Released: 2016-05-18 
• Deposition Author(s): Khoshnevis, S., Karbstein, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.283 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal Structure of the C-terminal domain of Rrp5

Khoshnevis, S., Karbstein, K.

(2016) PLoS Biol 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.08 kDa 
• Atom Count: 2,317 
• Modeled Residue Count: 276 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA biogenesis protein RRP5	A [auth B]	572	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RRP5, FMI1, YMR229C, YM9959.11C
UniProt
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05022  Go to UniProtKB:  Q05022

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.283 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.14	α = 90
b = 114.14	β = 90
c = 67.84	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
Aimless	data scaling
PHENIX	phasing
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Khoshnevis, S., Karbstein, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM086451

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references